Those are the ones that are masterpieces.
I have seen hundreds and hundreds of movies. Thats a pretty small list.
In fact, Blade Runner, My Neighbor Totoro, Grave of the Fireflies, Dr. Stragelove, Casablanca, The Great Dictator, Come and See, and others are also on Roger Ebert's Great Movies List.
Here are few examples of why I picked them. Dr. Zhivago for instance has a pretty run of the mill story when summarized, but the work on the sets, the cinematography (the use of mirrors is astounding), and the direction, make it an incredibly beautiful movie to watch. Grave of the Fireflies is perhaps the most emotionally powerful movie ever made, and Fireworks carefully deals with the trauma of losing a child and hopeless, and Millennium Actress combines beautiful images that just seem to flow perfectly with its score. Blade Runner doesn't really need explanation.
The godfather, for example, is a great movie. But it's a three-hour-long stretched melodrama in which you fall asleep halfway through! So no, I don't mean that kind of movie.
If a movie is so boring that you fall asleep, its not a great movie. I actually haven't seen Godfather so I can't really comment on it.